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In Silico Study of an Alzheimer’s disease protein (Aβ)
Plaque
Fibril Entanglement
Fibril
100nm
Aβ
1
AEDVGSNKGA
21
30
10nm
40
Aβ(21-30) Relevant to Development of AD
Experimental Background
• Experiments suggest Aβ(21-30) decapeptide may be the nucleating region for
folding of full Aβ(1-40) peptide.
What is the Question?
• To determine the fold of Aβ(21-30) with atomic detail and find the stabilizing
interactions.
How does it help?
• The fold of Aβ(21-30) may provide plausible scenarios for the initial stages of fibril
formation of full Aβ(1-40).
• Identification of amino acids important for folding stability may lead to strategies to
prevent fibril formation.
What did we Find?
• Aβ(21-30) adopts a loop conformation with center in S26, stabilized by hydrophobic
interactions between V24 and K28.
• There is a value for the strength of the electrostatic interaction that optimizes the
stability of the loop.
Experiments (our Collaborators)
Nuclear Magnetic Resonance data leads to two model structures of Aβ(21-30) in solution:
K28 below loop
K28 above loop
K28
K28
V24
S26
S26
V24
1. Aβ(21-30) adopts a loop conformation.
2. V24 and K28 are close.
3. The two model structures differ in the orientation of K28. Which one is true?
Lazo et at., submitted to J. Mol. Biol.
Simulations (my work)
Discrete Molecular Dynamics simulations of Aβ(21-30) in a cubic box of 40 Å with
periodic boundary conditions for 50ns.
• kBT=0.592 Kcal/mol (room temperature).
• We perform simulations for different electrostatic interaction (EI) strengths:
0.00 < EI < 1.5 Kcal/mol (typical in the surface of proteins)
1.50 < EI < 2.5 Kcal/mol (typical in the interior of proteins)
• Hydrogen-Bond strength = 3.5 Kcal/mol (typical in the surface of proteins)
• HP values in the range -9.3<HP<1.3 Kcal/mol (negative stands for repulsive)
Simulations Results
V24
K28
V-K Unpacked
V
V-K Packed
K
S26
Solvent Accesible Surface (Å2)
T.H.M.:
1. Hydrophobic interactions responsible for loop formation..
2. Electrostatic interaction of 1.5Kcal/mol optimizes loop stability.
Simulation Results (II)
E22
D23
K28
The unpacked conformations at EI=2.5Kcal/mol have strong electrostatic interactions!
E22···K28
p=0.23
D23···K28
p=0.48
E22···K28
D23···K28
p=0.29
Hypotheis for Future work: We hypothesize that Aβ(21-30) undergoes partial unpacking of
V24···K28 contacts and form D23···K28 electrostatic interactions upon fibril formation.
Simulation Results (III)
P() x 10-3
v
K28
n
S26

V24
(deg)
K28 below
loop plane
K28 above
loop plane
THM: Electrostatic interaction stabilizes K28 above the loop plane.
E22···K28
D23···K28
E22
D23
K28
Simulation Results (IV)
S
K
V
D
0.0
1.5
2.5
B1
7
11
B+
1
9
13
0.0
1.5
2.5
B1
6
5
B+
5
16
21
THM : only electrostatic interactions between E22 and K28 correlate with the orientation of
K28 above the loop.
Conclusions
• Aβ(21-30) adopts a loop conformation centered at S26,
stabilized by hydrophobic interactions between V24 and K28.
• There is a particular electrostatic interaction strength that
optimize the stability of the loop conformations.
V
S
K
D E
K
• Electrostatic interactions strengths typical of the interior of proteins destabilize the
loop conformations and form strong electrostatic interactions, preferentially
D23···K28.
Future Work
• Verify the hypothesis that Aβ(21-30) undergoes partial unfolding of V24-K28 and
formation of electrostatic interaction D23-K28 upon fibril formation with simulation
studies of many Ab(21-30).
Collaborators
Sergey V. Buldyrev#
Feng Ding†
Alfonso Lam Ng*
Manuel Marques§
Eugene Shakhnovich‡
Brigita Urbanc*
Luis Cruz*
Nikolay Dokholyan†
Noel Lazo¶
Shouyong Peng*
David B. Teplow ¶
Sijung Yun*
*Center for Polymer Studies and Dept of Physics, Boston Univ., Boston MA, USA.
†Dept of Biochemistry and Biophysics, School of Medicine, Univ. of North Carolina at Chapel Hill,
Chapel Hill NC, USA.
# Dept of Physics, Yeshiva University, New York NY, USA.
‡Department of Chemistry and Chemical Biology, Harvard Univ., Cambridge MA, USA
§ Dept. of Physics and Condensed matter C IV, Univ. Autonoma Madrid, Madrid, Spain.
¶Center for Neurological Diseases, Brigham and Women’s Hospital and Dept. of Neurology, Harvard
Medical School, Boston MA, USA
Ab Model
D23
A21
N27
G25
V24
E22
S26
K28
Three bonding types describe the protein geometry:
1
1st neigh.
(covalent)
21
4
3
1
2nd neigh.
(angle)
2
1
4
3
3rd neigh.
(dihedral)
2
4
3
G27
A30
-
Ab Model (cont.)
-
-
-
Three types of atomic interactions:
Hydrogen Bond
+
electrostatics
N
O
EI
hydropathy
+ N O
C
+ +
- -
+
-
HP
An Example of Dihedral Potential
Hydropathy Interactions
When two atoms i and j make a contact, they interact with a hydropathy strength.
HPij=HPi+HPj ,
HP : free energy of transfer
HP
Aqueous Phase
SAS :solvent accesible surface
HPi=ΔSASi · σi
Gas Phase
σ : atomic solvation parameter
Atomic Solvation Parameters
HPi=ΔSASi · σi
Arginine (R)
Lysine (K)
ΔFR=σC ·(ΣCi SASCi) + σN ·(ΣNi SASNi)
ΔFK=σC ·(ΣCi SASCi) + σN ·SASNi
Solve for σC and σN
Two Representative Conformations
K28 below loop plane
K28 above loop plane
E22-K28 interaction shown
Results: Loop Flexibility
σ
Δd
i
j
i
j
i
j
• The loop is rigid only when close to the turn
• E22-K28 and D23-K28 salt-bridges increase loop rigidity.
• When loop forms, distances E22-K28, D23-K28 and V24-K28 corresponding to attractive
interactions decrease the most.
• Flexibility of the loop strands allows K28 to flip-flop its orientation with respect to the loop